#!/bin/bash

source $DRAW_INI
source $DRAW_CFG

java -Xmx4g -jar $GATK \
  -T VariantEval \
  -R $REF_FASTA \
  --dbsnp $SNPDB \
  -et NO_ET \
  -EV CountVariants \
  -o ${2}/${1}.eval \
  --eval:${1} ${2}/${1}.vcf

EXITSTATUS=$?

if [ ! -s "${2}/${1}.eval" ];then echo "Missing ${2}/${1}.eval":exit 100;fi

exit $EXITSTATUS
